REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Ultra-LEAF purified anti-mouse CD169 (3D6.112)	BioLegend	Cat # 94019
Ultra-LEAF purified Rat IgG2a isotype control antibody (RTK2758)	BioLegend	Cat # 400543, RRID: AB_11148951
Fc block anti mouse-CD16/CD32 (93)	BioLegend	Cat # 101302, RRID: AB_312801
Anti-MLV Glycogag (mab34)	Santiago Lab/ Bruce Chesebro	Recognizes MLV (MA, p15) part of Glycogag (Chesebro et al., 1981)
Anti-MLV Gag p30 hybridoma (R187)	ATCC	Cat # CRL-1912
AF647 anti-MLV Glycogag (mab34)	Prepared in this work	N/A
FITC anti-mouse CD19 (6D5)	BioLegend	Cat # 115505, RRID: AB_313640
PE/Cy7 anti-mouse CD19(6D5)	BioLegend	Cat # 115519, RRID: AB_313654
APC anti-mouse CD4(RM4-5)	BioLegend	Cat # 100515, RRID: AB_312718
AF647 anti-mouse CD4 (GK1.5)	BioLegend	Cat # 100426, RRID: AB_493519
PE/Cy7 anti-mouse CD4 (GK1.5)	BioLegend	Cat # 100421, RRID: AB_312706
APC/Cy7 anti-mouse CD3ɛ (145-2C11)	BioLegend	Cat # 100329, RRID: AB_1877171
PE anti-mouse CD71 (RI7217)	BioLegend	Cat # 113807, RRID: AB_313568
APC/Cy7 anti-mouse TER-119 (TER-119)	BioLegend	Cat # 116223, RRID: AB_2137788
AF647 anti-mouse CD169 (3D6.112)	BioLegend	Cat # 142407, RRID: AB_2563620
PE anti-mouse CD169 (3D6.112)	BioLegend	Cat # 142403, RRID: AB_10915470
AF594 anti-mouse CD169 (3D6.112)	BioLegend	Cat # 142416, RRID: AB_2565620
FITC anti-mouse CD21/CD35 (CR2/CR1) (7E9)	BioLegend	Cat # 123407, RRID: AB_940403
PE anti-mouse CD23 (B3B4)	BioLegend	Cat # 101607, RRID: AB_312832
eFluor450 anti-mouse IgD, eBioscience (11-26c(11-26))	Invitrogen	REF # 48-5993-80, RRID: AB_1272239
Dylight 550 goat anti-mouse IgM cross-abosorbed secondary antibody	Invitrogen	Cat # SA5-10151, RRID: AB_2556731
PE anti-mouse CD45.1 (A20)	BioLegend	Cat # 110707, RRID: AB_313496
FITC anti-mouse CD45.2 (104)	BioLegend	Cat # 109805, RRID: AB_313442
APC anti-mouse/human CD44 (IM7)	BioLegend	Cat # 103011, RRID: AB_312962
InVivoMAb anti-mouse CD8α (YTS 169.4)	Bio X cell	Cat # BE0117, RRID: AB_10950145
AF488 anti-mouse CD8α (53-6.7)	BioLegend	Cat # 100723, RRID: AB_389304
AF647 anti-mouse CD107A (LAMP-1) (1D4B)	BioLegend	Cat #121609, RRID: AB_571990
PE anti-mouse Granzyme A (3G8.5)	BioLegend	Cat # 149703, RRID: AB_2565309
PE Anti-human/mouse Granzyme B Recombinant (QA16A02)	BioLegend	Cat # 372207, RRID: AB_2687031
PE anti-mouse IFNγ (XMG1.2)	BioLegend	Cat # 505807, RRID: AB_315401
PE anti-mouse CD279 (PD-1) (RMP1-30)	BioLegend	Cat # 109103, RRID: AB_313420
PE anti-mouse CD80 (16-10A1)	BioLegend	Cat # 104707, RRID: AB_313128
APC anti-mouse CD80 (16-10A1)	BioLegend	Cat # 104713, RRID: AB_313134
AF647 anti-mouse CD11c (N418)	BioLegend	Cat # 117314, RRID: AB_492850
APC/Cy7 anti-mouse CD11c (N418)	BioLegend	Cat # 117323, RRID: AB_830646
Alexa Fluor 647 anti-mouse/rat XCR1 (ZET)	BioLegend	Cat # 148213, RRID: AB_2564368
Alexa Fluor 647 anti-mouse CD11c	BioLegend	Cat # 117312, RRID: AB_389328
Bacterial and Virus Strains
Lactate dehydrogenase-elevating virus (LDV)-free FVC	Generated in this work by passaging the virus in BALB/cJ mice	N/A
FrMLV copackaged with MLV LTR Antares	Generated in this work	N/A
FrMLV co-packaged with MLV LTR GFP	Mothes Lab, Yale University	N/A
FVCYpet	Generated in this work	N/A
FVC GFP	Generated in this work	N/A
Chemicals, Peptides, and Recombinant Proteins
Liberase TL Research Grade	Sigma-Aldrich	Cat# 5401020001
DNAse I recombinant, RNAse-free	Roche	Ref # 04716728001
RPMI medium 1640 (1X)	Life technologies	Ref # 11875-093
Fetal bovine serum	Atlanta Biologicals	Cat # S11550
MEM Non-essential amino acid (NEAA) solution (100X)	Life technologies	Ref # 11140-050
Penicillin-streptomycin solution (10,000 U/ml)	Life technologies	Ref # 15140122
Sodium pyruvate (100 mM)	Life technologies	Ref # 11360-070
2-Mercaptoethanol	Sigma-Aldrich	Cat # M3148
L-Glutamine (200mM)	Life technologies	Ref # 25030-081
Red blood cell lysis buffer-Hybri-Max	Sigma-Aldrich	Cat # R7757-100ML
RBC Lysis Buffer (10X)	BioLegend	Cat # 420301
Dulbecco’s Phosphate Buffered Saline (DPBS) 1X	Life technologies	Ref # 14190-144
Hybridoma-SFM	Gibco	Cat # 12045-076
Ultra-low IgG FBS	Life technologies	Cat # 16250-086
Bovine Serum Albumin (BSA)	Sigma-Aldrich	Cat# A9647-100G CAS: 9048-46-8
Accutase	Biolegend	Cat # 423201
0.05% Trypsin-EDTA (1X)	Life Technologies	Cat # 25300-054
K3 EDTA 15% Solution	Fisher Scientific	Cat # BD 366450
Gelatin (Teleostean gelatin) Type A	Sigma-Aldrich	Cat # G7041 CAS: 9000-70-8
Triton-X 100 t-octyl phenoxy polyethoxyethanol	American Bioanalytical	Cat # AB02025-00500 CAS: 9002-93-1
PMA (phorbol 12-myristate-13-acetate)	Sigma	Cat # 19-144
Ionomycin	Sigma	Cat # I3909-1ML
GolgiStop	BD Biosciences	Cat # 554724
Brefeldin A	Sigma-Aldrich	Cat # B7651-5MG CAS: 20350-15-6
Paraformaldehyde (PFA)	Electron Microscopy Sciences	Cat # 19200 CAS: 30525-89-4
Rat serum	Stemcell Biotechnologies	Cat # 13551
L-lysine Monohydrochloride	Sigma-Aldrich	Cat # L1262
Sodium (meta)periodate	Sigma-Aldrich	Cat # 30323-100G CAS: 7790-28-5
Sucrose/ α-D-glucopyranosyl-β-D-fructofuranoside	americanBIO	Ref # AB01900-01000 CAS: 57-50-1
Tissue-Tek O.C.T Compound	Sakura	Cat # 4583
Fc receptor blocker	Innovex	Cat # NB335
ProLong Gold antifade reagent	Invitrogen	Cat # P36934
Glutaraldehyde	Electron Microscopy Sciences	Cat # 16220 CAS: 111-30-8
Sodium cacodylate trihydrate	Electron Microscopy Sciences	Cat #12300
Ficoll	Sigma-Aldrich	Cat #F2878-100g
Osmium tetroxide	Electron Microscopy Sciences	Cat #19110
Uranyl acetate	Electron Microscopy Sciences	Cat #22400
Acetone, EM-Grade, Glass-Distilled	Electron Microscopy Sciences	Cat #10015
Epon-Araldite resin	Electron Microscopy Sciences	Cat #13940
Lead citrate	Electron Microscopy Sciences	Cat #17800 CAS: 512-26-5
Gold beads (10 nm)	Ted Pella	Cat. #15703-1
Bouin’s solution	Sigma-Aldrich	Cat # HT10132-1L
FTY720	Cayman Chemical	Cat # 10006292 CAS: 162359-56-0
Dimethyl sulfoxide (DMSO)	Sigma-Aldrich	Cat # D2650-5X5ML CAS: 67-68-5
Sodium azide	Sigma-Aldrich	Cat # S-8032 EC No: 247-852-1
Sodium phosphate, Monobasic, Monohydrate, Crystal (NaH2PO4⋅H2O)	J.T.Baker	Cat # 3818-01 CAS: 10049-21-5
Sodium phosphate, Dibasic, Anhydrous (Na2HPO4)	J.T.Baker	Cat # 3828-01 CAS: 7558-79-4
Glycine	American Bioanalytical	Cat # AB00730-01000 CAS: 56-40-6
Passive lysis buffer (5X)	Promega	Cat # E194A
Guinea pig complement	MP Biomedical	Cat # 55854
DNase inactivation reagent	Ambion	Cat # 8173G
MLV specific peptide (GK1754) (KKCCLCLTVFL)	Genscript	N/A
FrMLV Gag peptide (CCLCLTVFL)	Peptide 2.0	N/A
Critical Commercial Assays
Mix-n-Stain CF 488A Antibody Labeling Kit (50-100μg)	Sigma-Aldrich	Cat # MX488AS100 SIGMA
Mix-n-Stain CF 647 Antibody Labeling Kit (50-100μg)	Sigma-Aldrich	Cat # MX647S100 SIGMA
Nano-Glo Luciferase Assay System	Promega	Cat # N1120
KAPA SYBR FAST qPCR Master Mix (2X) Kit	KAPA Biosystems	Cat # KK4600 and KK4601
Ambion DNase I (RNase-free)	Thermo Fisher Scientific	Cat # AM2222
RNeasy Mini Kit (50)	Qiagen	Cat #/ID 74104
qScript cDNA Synthesis Kit	Quanta Biosciences	Cat # 95047-100
Negative selection mouse CD4+ T cell enrichment kit	Stemcell technologies	Cat # 19752A
MojoSort mouse CD8 T cell isolation kit	BioLegend	Cat # 480008
Experimental Models: Cell Lines
Rat hybridoma mAb34	Santiago Lab/ Bruce Chesebro	Recognizes MLV (MA, p15) part of Glycogag (Chesebro et al., 1981)
HEK293	ATCC	Cat # CRL-1573
S49.1	ATCC	Cat # TIB-28
DFJ8	Mothes Lab (From Jim Cunningham, Dana Farber)	N/A
Experimental Models: Organisms/Strains
C57BL/6J (B6)	The Jackson Laboratory	The Jackson Laboratory Stock No: 000664
BALB/cJ	The Jackson Laboratory	The Jackson Laboratory Stock No: 000651
CD169-/- (B6 background)	Paul Crocker, University of Dundee UK	N/A
B6.A-Fv2s/s (B6 background)	The Francis Crick Institute, UK	Colony ID: GKAF
B6.A-Fv2s/sCD169-/- (B6 background)	Generated in this work	N/A
Ifnar1-/- (B6 background)	Iwasaki Lab, Yale University	MMRRC Stock No: 32045-JAX
Ifnar1-/-CD169-/- (B6 background)	Generated in this work	N/A
NagyDsRed.T3 (B6 background)	The Jackson Laboratory	Jackson Laboratory Stock No: 006051
UBI-GFP (B6 background)	The Jackson Laboratory	Jackson Laboratory Stock No: 004353
F-MuLV env-specific TCR-transgenic mouse (EF4.1 strain TCRβ transgenic mouse)	The Francis Crick Institute, UK	Colony ID: GKAA
Batf3-/- (B6 background)	Eisenbarth Lab, Yale University	Jackson Laboratory Stock No: 013755
Oligonucleotides
Mouse Actin, F: 5’-CATGTAGATGCACGACTAGCTTC-3’ R: 5’-GTTTCCTTGTTTAGCAGAACAGC-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse IFNB1, F: 5’-CTGGCTTCCATCATGAACAA-3’ R: 5’-AGAGGGCTGTGGTGGAGAA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse IFNA2, F: 5’-TCTGTGCTTTCCTCGTGATG-3’ R: 5’-TTGAGCCTTCTGGATCTGCT-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse IFNA4, F: 5’-GCAGAAGTCTGGAGAGCCCTC-3’ R: 5’-TGAGATGCAGTGTTCTGGTCC-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse IFITM3, F: 5’-CTGAAGGGGAGCGATTGATT-3’ R: 5’-AACGGCACATGACCAAAGAGTAGA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse IRF7, F: 5’-GCCAGGAGCAAGACCGTGTT-3’ R: 5’-TGCCCCACCACTGCCTGTA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse ISG15, F: 5’-GATTGCCCAGAAGATTGGTG -3’ R: 5’-TCTGCGTCAGAAAGACCTCA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse VIG1, F: 5’-AACCCCCGTGAGTGTCAACTA-3’ R: 5’-AACCAGCCTGTTTGAGCAGAA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse GBP4, F: 5’-TGGGGGACACAGGCTCTACA-3’ R: 5’-GCCTGCAGGATGGAACTCTCAA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse CXCL10, F: 5’-CCAAGTGCTGCCGTCATTTTC-3’ R: 5’-GGCTCGCAGGGATGATTTCAA-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse STAT1, F: 5’-CACATTCACATGGGTGGAAC-3’ R: 5’-TCTGGTGCTTCCTTTGGTCT-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse STAT2, F: 5’-ACCAGTGGGACCACTACAGC-3’ R: 5’-ATCTCAAGCTGCTGGCTCTC-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse IL10, F: 5’-CTCTTACTGACTGGCATGAGGAT-3’ R: 5’-GAGTCGGTTAGCAGTATGTTGT-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse 25OAS, F: 5’-ACTGTCTGAAGCAGATTGCG-3’ R: 5’-TGGAACTGTTGGAAGCAGTC-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Mouse MX1, F: 5’-AACCCTGCTACCTTTCAA-3’ R: 5’-AAGCATCGTTTTCTCTATTTC-3’	Yale School of Medicine, W. M. Keck Foundation, Oligo Synthesis Resource	N/A
Recombinant DNA
pLRB303-FrMLV	Mothes Lab, Yale University	N/A
pMMP-LTR-GFP	Mothes Lab, Yale University	N/A
pMIG-Antares	Generated in this work	N/A
pLRB303-FrMLVYpet	Generated in this work	N/A
pBR322-SFFV LS	Leonard Evans (NIH)	N/A
pLRB303-SFFV GFP	Generated in this work	N/A
pLRB303-GagGFP	Mothes Lab, Yale University	(Jin et al., 2009)
MLV GagPol	Mothes Lab, Yale University	N/A
pcDNA3-FrMLV Env	Mothes Lab, Yale University	N/A
Software and Algorithms
Accuri CSampler	BD Biosciences	N/A
FlowJo	Treestar	N/A
Volocity version 6.3	PerkinElmer	N/A
Photoshop CC	Adobe Systems	N/A
Illustrator CC	Adobe Systems	N/A
qPCR software	Biorad	N/A
Graphpad Prism	GraphPad Software	N/A
SerialEM software package	N/A	N/A
IMOD software package	N/A	N/A
Other
Luminometer	Berthold Technologies	N/A
Accuri C6	BD Biosciences	N/A
Leica Cryostat CM1950	Leica	CM1950 (Pietro Di Camilli Lab)
Leica TCS DMi8 SP8 microscope	Leica	CCMI Yale Central Facility
HPM-010 high-pressure freezing machine	Leica Microsystems, Vienna Austria	N/A
AFS-2 freeze-substitution machine	Leica Microsystems	N/A
Stereo dissecting microscope	Nikon	SMZ645
UC6 ultramicrotome	Leica Microsystems	N/A
Transmission electron microscope	Tecnai	TF30ST-FEG
2k x 2k CCD camera	Gatan, Inc	XP1000
C1000 Touch thermal cycler	Bio-Rad	N/A
CFX Connect Real-Time PCR Detection System	Bio-Rad	N/A
Nanodrop Spectrophotometer ND-1000	Thermo Fisher Scientific	N/A
27G × ½’’ insulin syringe with needle	TERUMO	Cat # SS∗05M2713
31G insulin syringe	BD Biosciences	Cat # 328468
70 μm Nylon cell strainer	FALCON	Cat # 352350
Acrodisc 25 mm Syringe Filter w/0.45 μm HT Tuffryn Membrane	PALL Life Sciences	Cat # 4184
HiTrap Protein G HP antibody purification columns	GE Healthcare Life Sciences	Cat # 29048581
Superfrost Plus Microscope Slides	Thermo Scientific	Cat # 4951PLUS-001
96-well white plates for luciferase assays	Costar	Cat # 3917
Accu-Edge High Profile Microtome Blades	SAKURA	Ref # 4685
Microcover glasses 1 ounce No.1	VWR	Cat # 48393 106
Tissue-Tek Cryomold	SAKURA	Ref # 4557
Brass planchettes	Ted Pella	Type A
Brass planchettes	Ted Pella	Type B
Cryotubes	Nunc	N/A
Teflon-coated glass microscope slides	N/A	N/A
Microsurgical scalpel	N/A	N/A
Plastic sectioning stubs	N/A	N/A
Diamond knife	Diatome, Ltd	N/A
Formvar-coated copper-rhodium slot grids	Electron Microscopy Sciences	N/A
Dual-axis tomography holder	E.A. Fischione Instruments, Export PA	Model 2040
Polystyrene Round-bottom Tube	FALCON	Ref # 352058
Optical Flat 8-Cap Strips for 0.2 ml tube stripes/plates	Bio-Rad	Cat # TCS0803
Individual PCR tubes 8-tube Strip, clear	Bio-Rad	Cat # TLS0801
ThermalGrid Rigid Strip PCR tubes	Denville Scientific	Ref # C18064
96 well U bottom plate	FALCON	Ref # 353077
Easy-Sep Magnet	Stemcell	Cat # 18000